"I think it was an amazing season," Harbaugh said. "In a lot of ways, beyond description. Incredible."
"I've said so often how proud I was of this team. I thought they played their hearts out," Harbaugh said. "I thought we were a well-coached team. They stand toe-to-toe and fight every time they go out onto the field."
Harbaugh is the first 49ers coach to win the award since the late Bill Walsh in 1981. Both Harbaugh and Walsh won the award after the Niners went 13-3 following 6-10 seasons.
Atlanta's Mike Smith is the last man to win the award in his initial season as an NFL head coach, in 2008.
"It didn't have the ending that we wanted," he said. "The football gods had a different ending in mind."
The Associated Press contributed to this report.